not compiling

[caonetto]

Any ideas what could be going on?
(repeatmodeler) cris@AWRIBIO02:/mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/work/installers/NINJA-0.98-cluster_only/NINJA$ make all g++ -std=gnu++11 -Wall -mssse3 -fopenmp -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include -c -o ArgumentHandler.o ArgumentHandler.cpp In file included from /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include/assert.h:5, from ExceptionHandler.hpp:8, from ArgumentHandler.hpp:4, from ArgumentHandler.cpp:7: /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’ 15 | typedef struct Except_Frame_T *Except_Frame_T; | ^~~~~~~~~~~~~~ /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’ 15 | typedef struct Except_Frame_T *Except_Frame_T; | ^~~~~~~~~~~~~~ /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’ 17 | Except_Frame_T prev; | ^~~~ /mnt/e70c0819-464b-4569-bbb6-cbc208b1daa1/cris/miniconda3/envs/funannotate/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace 16 | struct Except_Frame_T { | ^~~~~~~~~~~~~~ make: *** [<builtin>: ArgumentHandler.o] Error 1

[jebrosen]

Something you have installed through conda has provided a header file named assert.h or except.h, which has the same name but different contents from a system header file (the real assert.h should not reference an except.h). Conda has apparently configured the C++ compiler to treat the conda include/ directory as one of the "system directories".

This appears to have negatively affected several other projects as well. This should be reported to whatever project provides its own conflicting assert.h if we can figure out what that is, and/or to conda.

To solve this issue I would first try compiling NINJA in a fresh environment, or outside of conda entirely.

[caonetto]

Thanks for that, it compiled when running it outside conda environment.

CHeers.